Did significant numbers of Japanese officers escape prosecution during the Tokyo Trials?

Making a direct comparison between the Nuremberg and Tokyo trials is problematic. In an article in the European Journal of International Law (2010), Kirsten Sellars assessed the trials in the light of three academic texts published in 2008 & 2009:

From the outset, the Allies had justified the prosecution of the leaders of the Axis powers on the grounds that the conflict had been unique in the annals of warfare because of its totality and barbarity. This argument rested primarily upon a singular event: the Holocaust....

...Japan’s policies, by contrast, were unexceptional. Its leaders had certainly presided over wholesale assaults and terrible atrocities, but they had not broken the mould of international politics by instituting policies to systematically annihilate entire national, ethnic, racial or religious groups. As Bruno Simma noted in 1999: ‘Auschwitz was singularly German, and none of the offences committed by the Japanese political and military leaders came even close.'

That said,

To date, history’s verdict on Tokyo has not been favourable....

...the prosecuting powers at Tokyo violated the principle of legality by creating the new charge of crimes against peace, treated the war crimes charges as almost an afterthought, and breached the undertaking to give the accused a fair trial

...This emphasis arose because the lack of evidence linking defendants to specific events...

Prosecutors were hampered

...because of the empire-wide document destruction that the Imperial Japanese Government had orchestrated prior to effecting demobilisation.

For example, in a

directive (dated 20 August 1945) from Tokyo to respective Japanese Armies in Korea, Taiwan, Manchuria, China, Hong Kong, Thailand, Borneo, Malaya, and Java, the following instructions were given:

"Personnel who mistreated prisoners of war and internees or who are held in extremely bad sentiment by them are permitted to take care of it by immediately transferring or by fleeing without trace."

Australian officials in 1948 claimed that there was "extensive evidence" of not just of destroying records but also fabricated evidence and instructions to subordinates to lie.

There were certainly some high ranking officers and other officials who escaped punishment:

Perhaps the most notorious was Gen. Ishii of Unit 731, who escaped postwar prosecution in exchange, apparently, for supplying the U.S. government with details of his gruesome human experiments. Other suspected Japanese war criminals who were never indicted include three postwar prime ministers: Hatoyama Ichirō (1954–1956), Ikeda Hayato (1960–1964), and Kishi Nobusuke (1957). A convicted Class A war criminal, Shigemitsu Mamoru, a senior diplomat and foreign minister during the war years, regained the foreign minister portfolio in 1954.

Among others who escaped being charged were Lt. Gen. Kawabe Torashirō, Deputy Chief of Staff of the Imperial Japanese Army General Staff, and

...the notorious Col. Tsuji Masanobu,... the instigator behind the Bataan Death March.

However,

Despite the firm ruling of the United Nations War Crimes Commission (UNWCC) against it, investigators from an early stage tacitly implemented a superior orders defense. Thus the junior soldiers with the least amount of independent responsibility for atrocities would usually be passed over in favor of middle-ranking or more senior personnel.

This did not necessarily mean, though, that lower ranks were ignored, but the numbers involved meant choices had to be made. For example,

Some British authorities expected in October 1945 that around five hundred trials would be needed, but they still anticipated that the process could be completed by the end of July 1946....By early November 1945, British forces in Southeast Asia had a suspect list with 1,117 names, along with 925 names from other commands. By July 1946, the number of suspects in British custody had grown to about 7,600, presenting a formidable challenge of management.

Not surprisingly, many suspects fled if they were able to:

In Southeast Asia and China, some suspects joined the local nationalist or communist movements, though not all who did were suspected of war crimes. Some of those who were arrested managed to escape from custody; others committed suicide while in Allied hands.

With specific reference to the Burma Railway, it is evident that the British did not pursue low ranking suspects who could claim 'superior orders' unless

they were identified as individually vindictive. The corporals and sergeants who had issued orders to the guards were much more likely to be charged.